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Hsu-Che-Wei / COPILOT

Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
MIT License
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Do you have the cells' name of meristem, elongation and maturation? #2

Open duocang opened 3 years ago

duocang commented 3 years ago

Hi!

Thank you for the detailed analysis and heavily sequenced data.

Do you mind share cells' name of meristem, elongation and maturation?

I saw this data is available via GSE152766_Root_Atlas.rds.gz but I have no HPC access to deal with such data now.

I have checked GSE152766_Root_Atlas_spliced_unspliced_raw_counts.rds.gz, I was confused about the naming rule of cells.

>data <- readRDS("GSE152766_Root_Atlas_spliced_unspliced_raw_counts.rds")
>head(data@meta.data)
                                    orig.ident nCount_spliced_RNA nFeature_spliced_RNA nCount_unspliced_RNA
AAACCCAAGCCATTCA_1_1_1_1_1_1_1_1 SeuratProject              10032                 3899                 1695
AAACCCAAGCTGTTCA_1_1_1_1_1_1_1_1 SeuratProject              20531                 4064                 3054
AAACCCAAGGCGAACT_1_1_1_1_1_1_1_1 SeuratProject              22837                 4885                 2991
AAACCCACACCAGCCA_1_1_1_1_1_1_1_1 SeuratProject               8968                 2917                 1204
AAACCCACACTGGCGT_1_1_1_1_1_1_1_1 SeuratProject               7051                 2199                  832
AAACCCACAGACCTGC_1_1_1_1_1_1_1_1 SeuratProject              14501                 4566                 2217

Any special meaning of cell's name, like AAACCCAAGCCATTCA_1_1_1_1_1_1_1_1? I guess the alphabetic part is a read but what is the digital part?

Best regards Xuesong